Back in 2004, the Army hired Apptricity to create a software application that could keep track of where its soldiers deployed. The company delivered a handful of server and device licenses for $4.5 million that year, and the service purchased more about five years later.

The company found out their software was being copied after an Army official mentioned "thousands" of devices were running the software, during a presentation attended by Apptricity employees, according to the BBC.

And when the Army found out, the company alleged it tried covering its tracks.

"Apptricity discovered that ... the Army had engaged another contractor, Future Research Corporation of Huntsville, Alabama, to reverse engineer a portion of Apptricity's software application suite and proprietary framework architecture to replace certain infringed intellectual property rather than pay for the license shortfall," the complaint read.

The company went on to explain it found out through the Army providing them one of the reverse-engineered copies of the software.